Mercurial > repos > iuc > bcftools_plugin_missing2ref
diff test-data/check.vcf @ 0:5e9cf5308e97 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
| author | iuc |
|---|---|
| date | Wed, 06 Jul 2016 07:07:16 -0400 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/check.vcf Wed Jul 06 07:07:16 2016 -0400 @@ -0,0 +1,38 @@ +##fileformat=VCFv4.1 +##INFO=<ID=TEST,Number=1,Type=Integer,Description="Testing Tag"> +##FORMAT=<ID=TT,Number=A,Type=Integer,Description="Testing Tag, with commas and \"escapes\" and escaped escapes combined with \\\"quotes\\\\\""> +##INFO=<ID=DP,Number=1,Type=Integer,Description="read depth"> +##INFO=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases"> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> +##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth"> +##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood"> +##FILTER=<ID=q10,Description="Quality below 10"> +##FILTER=<ID=test,Description="Testing filter"> +##contig=<ID=1,assembly=b37,length=249250621> +##contig=<ID=3,assembly=b37,length=198022430> +##contig=<ID=4,assembly=b37,length=191154276> +##reference=file:///lustre/scratch105/projects/g1k/ref/main_project/human_g1k_v37.fasta +##readme=AAAAAA +##readme=BBBBBB +##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes"> +##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT A B +1 3062915 id3D GTTT G 12.9 q10 DP4=1,2,3,4;AN=4;AC=2 GT:GQ:DP:GL 0/1:409:35:-20,-5,-20 0/1:409:35:-20,-5,-20 +1 3062915 idSNP G T,C 12.6 test TEST=5;DP4=1,2,3,4;AN=4;AC=1,1 GT:TT:GQ:DP:GL 0/1:0,1:409:35:-20,-5,-20,-20,-5,-20 0/2:0,1:409:35:-20,-5,-20,-20,-5,-20 +1 3106154 . CAAA C 342 PASS AN=4;AC=2 GT:GQ:DP 0/1:245:32 0/1:245:32 +1 3106154 . G A 59.2 PASS AN=4;AC=1 GT:GQ:DP 0/1:245:32 0/0:245:32 +1 3157410 . G A 90.6 q10 AN=4;AC=4 GT:GQ:DP 1/1:21:21 1/1:21:21 +1 3162006 . G A 60.2 PASS AN=4;AC=3 GT:GQ:DP 1/1:212:22 0/1:212:22 +1 3177144 . GT G 45 PASS AN=4;AC=2 GT:GQ:DP 0/1:150:30 0/1:150:30 +1 3184885 . TAAAA TA,T 61.5 PASS AN=4;AC=2,2 GT:GQ:DP 1/2:12:10 1/2:12:10 +2 3199812 . G GTT,GT 82.7 PASS AN=4;AC=2,2 GT:GQ:DP 1/2:322:26 1/2:322:26 +3 3212016 . CTT C,CT 79 PASS AN=4;AC=2,2 GT:GQ:DP 1/2:91:26 1/2:91:26 +4 3258448 . TACACACAC T 59.9 PASS DP=62;AN=4;AC=2 GT:GQ:DP 0/1:325:31 0/1:325:31 +4 3258449 . GCAAA GA,G 59.9 PASS DP=62;AN=4;AC=2 GT:GQ:DP 0/1:325:31 0/1:325:31 +4 3258450 . AAAAGAAAAAG A,AAAAAAG 59.9 PASS DP=60;AN=4;AC=2 GT:GQ:DP 0/1:325:31 0/1:325:31 +4 3258451 . AAA AGT 59.9 PASS AN=4;AC=2 GT:GQ:DP 0/1:325:31 0/1:325:31 +4 3258452 . AAA AGA 59.9 PASS AN=4;AC=2 GT:GQ:DP 0/1:325:31 0/1:325:31 +4 3258453 . AACA AGA 59.9 PASS AN=4;AC=2 GT:GQ:DP 0/1:325:31 0/1:325:31 +4 3258453 . ACA AAGA 59.9 PASS AN=4;AC=2 GT:GQ:DP 0/1:325:31 0/1:325:31 +4 3258454 . AACA AACA 59.9 PASS AN=4;AC=2 GT:GQ:DP 0/1:325:31 0/1:325:31